Thanks for clarifying its purpose! I guess I do still have one question,
though: are ccp4 files computed via phenix.maps (from e.g., a .pdb and
.mtz) unsuitable for real-space refinement (e.g., some kind of structural
optimization with a scoring function that includes an electron density
term) because such a ccp4 file is itself influenced by the starting model?
On Wed, May 25, 2016 at 1:57 PM, Dale Tronrud <detBB at daletronrud.com> wrote:
>> An mtz file is a generic container for information that is
> represented as Fourier coefficients - amplitudes and/or phases. The mtz
> you get from data reduction contains your observed diffraction pattern.
> There are quite a variety of things that might be in there, e.g.
> intensities, amplitudes, indications of anomalous scattering.
>> The "map_coeffs" mtz probably echos all of those data and includes
> the amplitudes/phases which can be used to calculate several maps.
> These coefficients are derived from both your observations and the
> coordinates of your model that matches the "map_coeffs" file. The
> program could simply write a map file directly, but the Fourier
> representation takes less disk space and is quicker to read and write
> than a map.
>> The "map_coeffs" file is a "throw away" file. You use it to look at
> your map, but when you continue refinement you should always use the
> original mtz. You don't want to refine your model against an mtz that
> contains data calculated from your model. While it might be okay, it is
> safer to stick with the original.
>> Dale Tronrud
>> On 5/25/2016 10:38 AM, Andy Watkins wrote:
> > Thanks--that certainly makes sense. In that case, I suppose I have a
> > different question: what distinguishes the .mtz file suffixed
> > "map_coeffs," which is output by phenix.maps, from the input .mtz?
> >
> > On Wed, May 25, 2016 at 1:28 PM, Christian Roth
> > <christianroth034 at gmail.com <mailto:christianroth034 at gmail.com>> wrote:
> >
> > You might look for the Real space correlation coefficient to see if
> > your model fit that particular map better than before, but thats
> > probably it.
> >
> > There is no subset experimental data just influenced by one chain.
> > The whole complex contributes to each measurement and vice versa
> > your chain A model contribute to each measurement you made to
> > generate the maps. Sorry, but that's it
> >
> > Christian
> >
> > Am 25.05.2016 um 17:31 schrieb Andy Watkins:
> >> Perhaps necessary preface: I am largely learning as I go, and
> >> large parts of Phenix (and the details of refinement data file
> >> formats) are still black boxes for me.
> >>
> >> Suppose I have a model of one chain of a complex and an .mtz
> >> describing the entire complex. I have performed some refinement
> >> procedure altering the model of that single chain.
> >>
> >> My aim is to determine how this refinement procedure has affected
> >> the fit to the experimental data--or, really, the subset of the
> >> experimental data expected to be relevant for my model.
> >>
> >> For obvious reasons,
> >>
> >> phenix.model_vs_data chain_A.pdb whole_complex.mtz
> >> phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz
> >>
> >> are undesirable: they evaluate the model of a single chain against
> >> the whole complex's data, and there's obviously a lot of
> >> unsatisfied electron density. So, while this command /works/, it
> >> reports an unrepresentative fit. (In theory, one solution to my
> >> problem would be to re-combine each chain's refined version, then
> >> run model_vs_data on the recombined, refined complex. I'm
> >> interested nonetheless in how it would work on the chains
> separately.
> >>
> >> Now, during the refinement procedure, we of course generate .ccp4
> >> density maps for the individual chain models:
> >>
> >> phenix.maps chain_A.pdb whole_complex.mtz
> >>
> >> which produces the ccp4 file as well as, crucially,
> >> chain_A_map_coeffs.mtz. Attempting to employ that resulting .mtz
> >> file, i.e.
> >>
> >> phenix.model_vs_data chain_A.pdb whole_complex.mtz
> >> phenix.model_vs_data chain_A_refined.pdb whole_complex.mtz
> >>
> >> leads to an evocative error: Sorry_No_array_of_the_required_type:
> >> No reflection arrays available.
> >>
> >> My highest suspicion is that I need to alter maps.params in a
> >> particular way so that reflection arrays are also output to
> >> model_map_coeffs.mtz. I could also imagine that I need to be using
> >> another program entirely!
> >>
> >> Thanks in advance for whatever help you can provide;
> >> unfortunately, I can't provide any input files.
> >>
> >>
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